First, thank you very much for MaTeX, I'm a happy user and I love it.
Recently, MaTeX started throwing errors being unable to locate lmodern.sty. The reason was in an incorrectly set up path to pdflatex, and I quickly fixed it.
In more detail, now I have two installations of TeXLive on my Linux system. One is a full native install, and the second one is a small installation from arch repositories. I needed this second one because some other packages marked texlive as a mandatory dependence. As a result, in a shell, which pdflatex points to my native installation which has lmodern.sty. In Mathematica, it points to the packaged installation which doesn't have this package.
Of course, there are multiple ways to fix it, but it took me some time to figure out the reason, and I believe this exact situation deserves to be mentioned in the documentation.